A top U.S. official’s son who is working for a pro-democracy group in Egypt has been barred from leaving the country, along with at least five other Americans, escalating a crackdown on such groups by Egypt’s military government that has outraged the United States.

Sam LaHood, the son of Transportation Secretary Ray LaHood, said Thursday that he learned of the travel ban only when he was turned away from the Cairo airport Saturday. He is the director of the Egyptian program of the International Republican Institute (IRI), a Washington-based civil society organization.

IRI was one of three U.S.-based nonprofit groups in Cairo that were raided and shut down on Dec. 29 by Egyptian authorities, who accused the groups of using foreign funds to support unrest in Egypt.

After an outcry in Washington and in European capitals, the ruling generals appeared to retreat, promising President Obama and other top officials that the computers and other property confiscated from the three U.S.-based groups and at least four other nongovernmental organizations would be returned and their offices reopened.

But the offices remain closed, the equipment is still gone, and in an apparent escalation, a travel ban has been imposed on foreigners being investigated by the Egyptian government.

Sam Lahood, left, watches as his father Ray is sworn in as Transportation Secretary at the Transportation Department in Washington. Egypt has banned the son of Transportation Secretary LaHood and at least five other Americans from leaving the country, officials said Thursday. (Anonymous/AP)

As many as 40 foreigners are now on a travel ban list as a result of the Egyptian investigation, said Scott Mastic, IRI’s regional director for the Middle East and North Africa.

“It’s absolutely an escalation,” Mastic said of the bans, which were first reported by Politico on Wednesday evening. “To have a strategic U.S. ally issue bans against American citizens is deeply troubling.”

Employees of IRI, the Washington-based National Democratic Institute and Freedom House have been called in several times for questioning focused on foreign funding and the legality of their presence in Egypt. IRI said it was told by Egyptian judicial officials that if the case goes to court, trials would begin next month. A judicial official who spoke on the condition of anonymity confirmed that time frame.

“The implication is that these persons will be put on a list because there is an attempt to move to formally charge them and put people on trial,” Mastic said. “We are absolutely worried for their well-being.”

U.S. officials say they have pressed Egypt on the issue repeatedly and forcefully in almost daily conversations between the U.S. Embassy and the Egyptian government. This weekend, Secretary of State Hillary Rodham Clinton raised the issue in a call with Egypt’s foreign minister. President Obama also brought up the rights of NGOs specifically in a phone call last week.

“They are asserting that these people are subject to the judicial process, and so is the equipment,” said State Department spokeswoman Victoria Nuland. “Our point is that whatever the formalities are here, they need to be concluded as quickly as possible.”

Sen. John McCain (R-Ariz.) also issued a statement, calling Egypt’s actions “outrageous.”

NGO workers appeared startled Thursday that Egypt’s military council, the largest recipient of U.S. aid, is willing to clash with its U.S. allies over American pro-democracy organizations working in the country.

“This is a very serious escalation, and it shows all NGOs are very vulnerable,” said Heba Morayef, an Egypt researcher for Human Rights Watch in Cairo.

In private, State Department officials have also told Egypt that its actions are jeopardizing U.S. aid to Egypt’s military, said Charles Dunne, the director of Middle East and North Africa programming for Freedom House. U.S. military aid to Egypt totals more than $1.3 billion a year.

Dunne said that so far he is unaware of any travel bans on Freedom House employees in Cairo, all of whom are Egyptian.

Despite the State Department’s intervention, the Egyptian government has given no sign of backing off its investigation of the American groups. Judging by recent questions directed to NGO members by Egyptian interrogators, it instead seems to be preparing to charge the groups with not registering their organizations and with providing foreign funding, the groups’ leaders say.

Both IRI and NDI applied for registration to work in Egypt during former president Hosni Mubarak’s rule but were told that the paperwork would probably never go through. To suppress dissent, Mubarak kept a tight lid on the work of civil society organizations. After Egypt’s uprising a year ago, Mastic said, the U.S. government encouraged IRI to begin democracy-building programs, and the issue has become a major point of friction between the United States and Egypt’s military rulers.

IRI and NDI renewed their registration applications recently at the request of the Egyptian government.

“It’s gotten more serious,” Sam LaHood said Thursday, referring to the travel ban. According to IRI’s leaders in Washington, four of the group’s Cairo employees have been barred from traveling, including LaHood, two other Americans and a European.

“The reality is, this is bigger than me or IRI,” LaHood said. “There are 300 NGOs being investigated by the Egyptian government, and only a handful of them are American.”

Leslie Campbell, NDI’s regional director for the Middle East and North Africa, said that the organization was verbally notified Thursday of a travel ban on six employees — three Americans, two Serbians and a Bosnian — after it heard about LaHood being turned away at the airport and requested information.

“It’s very worrying,” Campbell said, adding that the organization took it as a sign that the six could be charged in the investigation into foreign funding. “We have done our best to be transparent with the Egyptian government.”

Authorities stormed 17 offices in all last month, including some operated by Germany’s Konrad Adenauer Foundation and at least two Egyptian nongovernmental organizations: the Arab Center for Independence of Justice and Legal Professions and the Budgetary and Human Rights Observatory.

NDI and IRI are democracy-building groups backed by the U.S. government that operate globally. Both have been monitoring Egypt’s ongoing, multi-phase parliamentary elections. Freedom House advocates for democracy, political freedoms and human rights.

By investigating the groups, Egypt’s embattled military chiefs appear to be trying to prove that foreign organizations have been funding and orchestrating recent waves of anti-government protests, in which scores have been killed and hundreds wounded.

A year after the citizen revolt that pushed Mubarak from power, many Egyptians have resumed demonstrating, saying that the caretaker military government has adopted many repressive Mubarak-era tactics. They are calling for a faster transition to civilian government and for immediate reforms to protect individual rights and freedoms.

The U.S. Congress has adopted a resolution that will not allow military aid to Egypt to continue without a certification that the government is carrying out a democratic transition. Michael Posner, assistant secretary of state for human rights, labor and democracy, said in Cairo on Thursday that one of the key benchmarks Congress is looking at is freedom of association.

“We are greatly concerned that organizations like IRI, NDI and Freedom House ought to be able to operate,” he told a news conference.

White House officials would not comment on the travel ban and also declined to say whether the administration is making any new efforts to secure Sam LaHood’s safe departure from Egypt. Ray LaHood also would not comment “due to the sensitivity of the situation,” a Department of Transportation spokesman said.

The transportation secretary is due to appear Friday in Tampa for an event on economic development and infrastructure policy tied to Obama’s State of the Union address.

Staff writers William Wan, Ed O’Keefe and Ashley Halsey III in Washington contributed to this report.